broadinstitute / gamgee / 1421

Pull #376

travis-ci

Edits based on suggestions by Joel and David
1. VariantHeaderMerger accepts both shared_ptr<bcf_hdr_t> and
VariantHeader& as inputs. To do this, VariantHeaderMerger
is now a friend of VariantHeader so that m_header can be directly
accessed.
2. Created two VariantHeaderMerger variants optimized for two different
purposes
  a. InputOrderedVariantHeaderMerger - fast traversal of all fields for
a single input VCF
  a. FieldOrderedVariantHeaderMerger - fast traversal of all input VCFs
for a single field
Created more rigorous tests
3. Use static const int members instead of #define
4. Use different VCFs with different headers in the tests
5. Store shared_ptr<bcf_hdr_t> within VariantHeaderMerger. Use raw
pointers only when needed
6. Added a get_input_vcf_headers() function for MultipleVariantReader
7. Missing values in VariantHeaderMerger are now represented by
bcf_int32_missing instead of -1
8. Made validate_header() private in MultipleVariantReader again.

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